[Now, any in-depth discussion will probably necessitate a warning of spoilers. You've been properly notified.]
Here's how you enjoy Prometheus: don't ask, "Why?" sit back, and enjoy the gorgeous design of the movie. Because it is gorgeous, and recalls the great design work that marked Alien in so many ways.
The idea of making a prequel to Alien
has apparently been kicking around for a while, but it's here now, even
though Ridley Scott and Damon Lindelof always go out of their way to
contend that Prometheus isn't strictly an Alien prequel in promotions and interviews...